Contacts of the helix formed by residues 144 - 160 (chain A) in PDB entry 2W93
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ASP* 3.3 24.2 + - - +
143A ALA* 1.3 82.0 - - + +
145A ALA* 1.3 64.6 + - - +
146A PRO* 3.4 3.6 - - - -
147A ALA* 3.3 12.9 + - - +
148A GLU* 3.0 32.3 + - - +
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.6 25.8 - - + -
139A ILE* 3.8 29.1 - - + +
141A ASP 3.1 16.2 + - - +
142A ILE* 3.6 8.3 - - - +
144A THR* 1.3 77.9 - - - +
146A PRO* 1.3 71.6 - - + +
148A GLU* 3.1 2.6 + - - +
149A ILE* 2.9 26.7 + - + +
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Residues in contact with PRO 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.5 3.4 - - + -
9A TYR* 3.7 24.9 - - + +
142A ILE 3.5 11.7 - - - +
143A ALA 4.3 6.1 - - - +
144A THR 3.6 2.7 - - - -
145A ALA* 1.3 92.5 - - + +
147A ALA* 1.3 61.5 + - - +
149A ILE* 3.3 2.5 + - + +
150A ASP* 2.9 29.6 + - - +
176A VAL* 3.7 26.9 - - + -
177A PRO* 5.4 1.1 - - + -
180A LEU* 3.6 30.5 - - + -
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A THR* 3.3 15.1 + - - +
146A PRO* 1.3 80.3 - - - +
148A GLU* 1.3 60.6 + - + +
150A ASP* 3.3 8.7 + - - +
151A ARG* 2.9 28.9 + - - +
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ALA* 3.4 12.5 - - + +
139A ILE* 3.5 28.7 - - + +
144A THR* 3.0 25.2 + - - +
145A ALA 3.1 3.3 + - - +
147A ALA* 1.3 75.8 - - + +
149A ILE* 1.3 59.3 + - - +
151A ARG* 2.8 48.4 + - - +
152A CYS* 2.9 34.6 + - - -
165A LEU* 5.1 0.2 - - - -
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.5 42.0 - - + +
9A TYR* 3.9 24.9 - - + -
10A LEU* 4.0 24.2 - - + -
13A ARG* 4.7 1.1 - - + -
139A ILE* 5.3 1.1 - - + -
145A ALA* 2.9 12.5 + - + +
146A PRO 3.6 6.3 - - - +
148A GLU* 1.3 76.1 - - - +
150A ASP* 1.3 64.1 + - - +
152A CYS* 3.2 7.0 + - - +
153A ILE* 2.9 43.3 + - + +
165A LEU* 4.0 23.7 - - + +
167A LEU* 4.8 9.0 - - + -
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 2.7 27.7 + - - -
13A ARG* 2.9 37.2 + - - +
146A PRO 2.9 15.0 + - - +
147A ALA* 3.5 7.6 - - - +
149A ILE* 1.3 76.0 - - - +
151A ARG* 1.3 56.6 + - - +
153A ILE 3.4 0.3 + - - -
154A ARG* 2.9 31.4 + - - +
185A ILE* 3.7 25.7 - - + +
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Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A THR* 3.0 34.9 + - - +
136A THR 3.1 23.0 + - - -
137A ALA* 3.7 6.5 - - - +
147A ALA 2.9 17.2 + - - +
148A GLU* 2.8 44.3 + - - +
150A ASP* 1.3 77.7 - - - +
152A CYS* 1.3 59.9 + - - +
154A ARG* 3.8 5.1 - - - +
155A THR* 2.9 41.7 + - - +
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Residues in contact with CYS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 3.9 11.9 - - + -
135A THR* 5.0 1.3 - - - -
136A THR 4.8 0.4 - - - -
137A ALA* 3.7 29.2 - - - -
148A GLU 2.9 19.5 + - - +
149A ILE* 3.2 6.7 + - - +
151A ARG* 1.3 84.0 - - - +
153A ILE* 1.3 54.7 + - - +
155A THR* 3.4 3.0 + - - -
156A THR* 2.7 39.5 + - - -
163A VAL* 3.7 26.8 - - + +
164A TYR 4.4 1.1 - - - -
165A LEU* 4.1 16.2 - - + -
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Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.5 3.1 - - + -
13A ARG* 3.7 30.1 - - + -
14A LEU* 4.2 20.4 - - + +
17A VAL* 3.9 14.6 - - + -
67A MET* 4.0 7.6 - - + +
96A LEU* 4.0 18.8 - - + -
149A ILE* 2.9 31.8 + - + +
150A ASP 3.9 2.9 - - - +
152A CYS* 1.3 73.6 - - - +
154A ARG* 1.3 69.3 + - - +
156A THR* 3.4 8.0 + - - -
157A TYR* 3.2 19.1 + - - +
165A LEU* 6.3 0.2 - - + -
185A ILE* 3.8 17.3 - - + -
187A MET* 3.9 18.1 - - + +
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ASP 2.9 18.2 + - - +
151A ARG* 3.8 6.3 - - - +
153A ILE* 1.3 76.9 - - - +
155A THR* 1.3 60.4 + - - +
157A TYR* 3.1 2.9 + - - -
158A VAL* 2.9 50.3 + - + +
185A ILE* 3.9 6.0 - - + +
186A ASP* 2.8 57.7 + - - +
187A MET* 3.8 11.4 - - - -
188A SER 2.7 33.3 + - - +
189A LEU* 4.6 1.0 - - - +
190A LYS* 3.6 35.3 - - - +
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Residues in contact with THR 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLU* 3.6 30.1 - - + -
135A THR* 3.8 22.4 - - + +
151A ARG* 2.9 27.3 + - - +
152A CYS 3.9 3.1 - - - -
154A ARG* 1.3 77.1 - - - +
156A THR* 1.3 59.9 + - - +
158A VAL* 4.1 7.9 - - + -
159A THR* 2.7 40.3 + - + +
163A VAL* 3.9 2.9 - - + -
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Residues in contact with THR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A MET* 4.0 15.7 - - + -
94A GLY* 3.2 37.1 - - - +
95A VAL 3.5 13.7 - - - +
96A LEU* 3.7 10.3 - - - +
152A CYS 2.7 22.0 + - - -
153A ILE 3.6 5.6 - - - -
154A ARG 3.3 0.2 - - - -
155A THR* 1.3 75.8 - - - +
157A TYR* 1.3 58.7 + - - +
160A GLN* 3.0 28.6 + - - -
161A ARG 3.5 12.0 + - - +
163A VAL* 3.2 18.7 - - - +
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLY* 3.5 37.1 - - - -
67A MET* 3.9 13.5 - - + -
153A ILE 3.2 1.9 + - - +
154A ARG 3.1 4.7 + - - +
156A THR* 1.3 79.1 - - - +
158A VAL* 1.3 67.2 + - + +
160A GLN* 3.0 32.0 + - - +
187A MET* 3.3 57.7 - - + -
225A HIS* 5.5 0.2 + - - -
226A ASP* 5.8 4.2 - - - +
604A PY0 4.1 27.8 + - - -
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 2.9 59.7 + - + +
155A THR* 4.0 8.5 - - - +
157A TYR* 1.3 79.4 - - + +
159A THR* 1.3 72.3 + - + +
187A MET* 3.7 25.1 - - - +
188A SER 4.2 2.7 - - - +
189A LEU* 4.1 26.3 - - + +
225A HIS* 3.7 15.6 + - - -
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A HIS* 4.3 6.8 + - - -
134A GLU* 3.5 41.4 - - + +
155A THR* 2.7 28.8 + - + +
158A VAL* 1.3 86.7 - - + +
160A GLN* 1.3 69.8 + - - +
161A ARG* 3.3 19.2 + - - +
225A HIS* 4.3 6.1 + - - -
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Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA 5.0 2.9 - - - +
66A GLY 2.9 27.7 + - - +
92A HIS* 2.8 38.9 - - + +
93A VAL* 3.7 11.0 - - - +
94A GLY* 3.0 20.8 + - - +
156A THR 3.0 10.8 + - - -
157A TYR* 3.0 35.3 + - - +
158A VAL 3.4 0.2 - - - -
159A THR* 1.3 80.2 - - - +
161A ARG* 1.3 56.5 + - - +
224A ARG* 3.9 29.2 + - + +
225A HIS* 3.8 24.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il